• CAR-T Cells Targeting Epstein-Barr Virus gp350 Validated in a Humanized Mouse Model of EBV Infection and Lymphoproliferative Disease.

      Slabik, Constanze; Kalbarczyk, Maja; Danisch, Simon; Zeidler, Reinhard; Klawonn, Frank; Volk, Valery; Krönke, Nicole; Feuerhake, Friedrich; Ferreira de Figueiredo, Constanca; Blasczyk, Rainer; et al. (Elsevier (Cell Press), 2020-08-08)
      Epstein-Barr virus (EBV) is a latent and oncogenic human herpesvirus. Lytic viral protein expression plays an important role in EBV-associated malignancies. The EBV envelope glycoprotein 350 (gp350) is expressed abundantly during EBV lytic reactivation and sporadically on the surface of latently infected cells. Here we tested T cells expressing gp350-specific chimeric antigen receptors (CARs) containing scFvs derived from two novel gp350-binding, highly neutralizing monoclonal antibodies. The scFvs were fused to CD28/CD3ζ signaling domains in a retroviral vector. The produced gp350CAR-T cells specifically recognized and killed gp350+ 293T cells in vitro. The best-performing 7A1-gp350CAR-T cells were cytotoxic against the EBV+ B95-8 cell line, showing selectivity against gp350+ cells. Fully humanized Nod.Rag.Gamma mice transplanted with cord blood CD34+ cells and infected with the EBV/M81/fLuc lytic strain were monitored dynamically for viral spread. Infected mice recapitulated EBV-induced lymphoproliferation, tumor development, and systemic inflammation. We tested adoptive transfer of autologous CD8+gp350CAR-T cells administered protectively or therapeutically. After gp350CAR-T cell therapy, 75% of mice controlled or reduced EBV spread and showed lower frequencies of EBER+ B cell malignant lymphoproliferation, lack of tumor development, and reduced inflammation. In summary, CD8+gp350CAR-T cells showed proof-of-concept preclinical efficacy against impending EBV+ lymphoproliferation and lymphomagenesis.
    • Carbonic anhydrase subunits form a matrix-exposed domain attached to the membrane arm of mitochondrial complex I in plants.

      Sunderhaus, Stephanie; Dudkina, Natalya V; Jänsch, Lothar; Klodmann, Jennifer; Heinemeyer, Jesco; Perales, Mariano; Zabaleta, Eduardo; Boekema, Egbert J; Braun, Hans-Peter; Institut für Angewandte Genetik, Universität Hannover, Herrenhäuser Strasse 2, D-30419 Hannover, Germany. (2006-03-10)
      Complex I of Arabidopsis includes five structurally related subunits representing gamma-type carbonic anhydrases termed CA1, CA2, CA3, CAL1, and CAL2. The position of these subunits within complex I was investigated. Direct analysis of isolated subcomplexes of complex I by liquid chromatography linked to tandem mass spectrometry allowed the assignment of the CA subunits to the membrane arm of complex I. Carbonate extraction experiments revealed that CA2 is an integral membrane protein that is protected upon protease treatment of isolated mitoplasts, indicating a location on the matrix-exposed side of the complex. A structural characterization by single particle electron microscopy of complex I from the green alga Polytomella and a previous analysis from Arabidopsis indicate a plant-specific spherical extra-domain of about 60 A in diameter, which is attached to the central part of the membrane arm of complex I on its matrix face. This spherical domain is proposed to contain a heterotrimer of three CA subunits, which are anchored with their C termini to the hydrophobic arm of complex I. Functional implications of the complex I-integrated CA subunits are discussed.
    • Case-Centred Multidimensional Scaling for Classification Visualisation in Medical Diagnosis

      Klawonn, Frank; Lechner, Werner M.; Grigull, Lorenz; Bioinformatics and Statistics, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany (2013-03)
    • Chemical Conjugation of a Purified DEC-205-Directed Antibody with Full-Length Protein for Targeting Mouse Dendritic Cells In Vitro and In Vivo.

      Volckmar, Julia; Knop, Laura; Hirsch, Tatjana; Frentzel, Sarah; Erck, Christian; van Ham, Marco; Stegemann-Koniszewski, Sabine; Bruder, Dunja; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (MyJove Corporation, 2021-02-05)
      Targeted antigen delivery to cross-presenting dendritic cells (DC) in vivo efficiently induces T effector cell responses and displays a valuable approach in vaccine design. Antigen is delivered to DC via antibodies specific for endocytosis receptors such as DEC-205 that induce uptake, processing, and MHC class I- and II-presentation. Efficient and reliable conjugation of the desired antigen to a suitable antibody is a critical step in DC targeting and among other factors depends on the format of the antigen. Chemical conjugation of full-length protein to purified antibodies is one possible strategy. In the past, we have successfully established cross-linking of the model antigen ovalbumin (OVA) and a DEC-205-specific IgG2a antibody (αDEC-205) for in vivo DC targeting studies in mice. The first step of the protocol is the purification of the antibody from the supernatant of the NLDC (non-lymphoid dendritic cells)-145 hybridoma by affinity chromatography. The purified antibody is activated for chemical conjugation by sulfo-SMCC (sulfosuccinimidyl 4-[N-maleimidomethyl] cyclohexane-1-carboxylate) while at the same time the sulfhydryl-groups of the OVA protein are exposed through incubation with TCEP-HCl (tris (2-carboxyethyl) phosphine hydrochloride). Excess TCEP-HCl and sulfo-SMCC are removed and the antigen is mixed with the activated antibody for overnight coupling. The resulting αDEC-205/OVA conjugate is concentrated and freed from unbound OVA. Successful conjugation of OVA to αDEC-205 is verified by western blot analysis and enzyme-linked immunosorbent assay (ELISA). We have successfully used chemically crosslinked αDEC-205/OVA to induce cytotoxic T cell responses in the liver and to compare different adjuvants for their potential in inducing humoral and cellular immunity following in vivo targeting of DEC-205+ DC. Beyond that, such chemically coupled antibody/antigen conjugates offer valuable tools for the efficient induction of vaccine responses to tumor antigens and have been proven to be superior to classical immunization approaches regarding the prevention and therapy of various types of tumors.
    • Chronic lung inflammation primes humoral immunity and augments antipneumococcal resistance.

      Boehme, Julia D; Stegemann-Koniszewski, Sabine; Autengruber, Andrea; Peters, Nicole; Wissing, Josef; Jänsch, Lothar; Jeron, Andreas; Bruder, Dunja; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017-07-10)
      Airway epithelial cells (AECs) display remarkable plasticity in response to infectious stimuli and their functional adaptations are critical for antimicrobial immunity. However, the roles of AECs and humoral mediators to host defense in non-communicable lung inflammation remain elusive. We dissected pulmonary defense against Streptococcus pneumoniae in hosts with pre-existing inflammatory conditions (SPC-HAxTCR-HA mice). Lung tissue transcriptomics and bronchoalveolar lavage fluid (BALF) proteomics revealed an induction of humoral defense mechanisms in inflamed lungs. Accordingly, besides antibacterial proteins and complement components being overrepresented in inflamed lungs, elevated polymeric immunoglobulin receptor (pIgR)-expression in AECs correlated with increased secretory immunoglobulin (SIg) transport. Consequently, opsonization assays revealed augmented pneumococcal coverage by SIgs present in the BALF of SPC-HAxTCR-HA mice, which was associated with enhanced antipneumococcal resistance. These findings emphasize the immunologic potential of AECs as well as their central role in providing antibacterial protection and put forward pIgR as potential target for therapeutic manipulation in infection-prone individuals.
    • Chronic Toxoplasma infection is associated with distinct alterations in the synaptic protein composition.

      Lang, Daniel; Schott, Björn H; van Ham, Marco; Morton, Lorena; Kulikovskaja, Leonora; Herrera-Molina, Rodrigo; Pielot, Rainer; Klawonn, Frank; Montag, Dirk; Jänsch, Lothar; et al. (2018-08-01)
      Chronic infection with the neurotropic parasite Toxoplasma gondii has been implicated in the risk for several neuropsychiatric disorders. The mechanisms, by which the parasite may alter neural function and behavior of the host, are not yet understood completely. Here, a novel proteomic approach using mass spectrometry was employed to investigate the alterations in synaptic protein composition in a murine model of chronic toxoplasmosis. In a candidate-based strategy, immunoblot analysis and immunohistochemistry were applied to investigate the expression levels of key synaptic proteins in glutamatergic signaling. A comparison of the synaptosomal protein composition revealed distinct changes upon infection, with multiple proteins such as EAAT2, Shank3, AMPA receptor, and NMDA receptor subunits being downregulated, whereas inflammation-related proteins showed an upregulation. Treatment with the antiparasitic agent sulfadiazine strongly reduced tachyzoite levels and diminished neuroinflammatory mediators. However, in both conditions, a significant number of latent cysts persisted in the brain. Conversely, infection-related alterations of key synaptic protein levels could be partly reversed by the treatment. These results provide evidence for profound changes especially in synaptic protein composition in T. gondii-infected mice with a downregulation of pivotal components of glutamatergic neurotransmission. Our results suggest that the detected synaptic alterations are a consequence of the distinct neuroinflammatory milieu caused by the neurotropic parasite.
    • Clarithromycin Exerts an Antibiofilm Effect against rdar Biofilm Formation, and Transforms the Physiology towards an Apparent Oxygen-depleted Energy and Carbon Metabolism.

      Zafar, Munira; Jahan, Humera; Shafeeq, Sulman; Nimtz, Manfred; Jänsch, Lothar; Römling, Ute; Choudhary, M Iqbal; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (ASM, 2020-08-24)
      Upon biofilm formation, production of extracellular matrix components and alteration in physiology and metabolism allows bacteria to build up multicellular communities which can facilitate nutrient acquisition during unfavorable conditions and provide protection towards various forms of environmental stresses to individual cells. Thus, bacterial cells become tolerant against antimicrobials and the immune system within biofilms. In the current study, we evaluated the antibiofilm activity of the macrolides clarithromycin and azithromycin. Clarithromycin showed antibiofilm activity against rdar (red, dry and rough) biofilm formation of the gastrointestinal pathogen Salmonella typhimurium ATCC14028 Nalr at 1.56 μM subinhibitory concentration in standing culture and dissolved cell aggregates at 15 μM in a microaerophilic environment suggesting that the oxygen level affects the activity of the drug. Treatment with clarithromycin significantly decreased transcription and production of the rdar biofilm activator CsgD, with biofilm genes such as csgB and adrA to be consistently downregulated. While fliA and other flagellar regulon genes were upregulated, apparent motility was downregulated. RNA sequencing showed a holistic cell response upon clarithromycin exposure, whereby not only genes involved in the biofilm-related regulatory pathways, but also genes that likely contribute to intrinsic antimicrobial resistance, and the heat shock stress response were differentially regulated. Most significantly, clarithromycin exposure shifts the cells towards an apparent oxygen- and energy- depleted status, whereby the metabolism that channels into oxidative phosphorylation is downregulated, and energy gain by degradation of propane 1,2-diol, ethanolamine and L-arginine catabolism, potentially also to prevent cytosolic, is upregulated. This analysis will allow the subsequent identification of novel intrinsic antimicrobial resistance determinants.
    • Collection and analysis of salivary proteins from the biting midge Culicoides nubeculosus (Diptera: Ceratopogonidae).

      Langner, Kathrin F A; Darpel, Karin E; Denison, Eric; Drolet, Barbara S; Leibold, Wolfgang; Mellor, Philip S; Mertens, Peter P C; Nimtz, Manfred; Greiser-Wilke, Irene; USDA-ARS, Arthropod-Borne Animal Diseases Research Laboratory, 1000 E. University Ave., Laramie, WY 82071, USA. klangner@uwyo.edu (2007-03)
      Salivary proteins of hematophagous Culicoides spp. are thought to play an important role in pathogen transmission and skin hypersensitivity. Analysis of these proteins, however, has been problematic due to the difficulty in obtaining adequate amounts of secreted Culicoides saliva. In the current study, a collection method for midge saliva was developed. Over a 3-d period, 3- to 5-d-old male and female Culicoides nubeculosus Meigen (Diptera: Ceratopogonidae) were repeatedly placed onto the collection system and allowed to deposit saliva into a filter. Salivary products were eluted from the filters and evaluated by gel electrophoresis and mass spectrometry as well as by intradermal testing and determination of clotting time. Gel electrophoresis revealed approximately 55 protein spots displaying relative molecular masses from 5 to 67 kDa and isoelectric points ranging from 4.5 to 9.8. The majority of molecular species analyzed by mass spectrometry showed high convergence with salivary proteins recently obtained from a cDNA library of Culicoides sonorensis Wirth & Jones, including proteins involved in sugarmeal digestion, defense, and coagulation inhibition as well as members of the D7 family and unclassified salivary proteins. In addition, the proteome analysis revealed a number of peptides that were related to proteins from insect species other than Culicoides. Intradermal injection of the saliva in human skin produced edema, vasodilatation, and pruritus. The anticoagulant activity of the saliva was demonstrated by significantly prolonged clotting times for human platelets. The potential role of the identified salivary proteins in the transmission of pathogens and the induction of allergies is discussed.
    • Common pre-diagnostic features in individuals with different rare diseases represent a key for diagnostic support with computerized pattern recognition?

      Grigull, Lorenz; Mehmecke, Sandra; Rother, Ann-Katrin; Blöß, Susanne; Klemann, Christian; Schumacher, Ulrike; Mücke, Urs; Kortum, Xiaowei; Lechner, Werner; Klawonn, Frank; et al. (Public Library of Science (PLoS), 2019-10-10)
      BACKGROUND: Rare diseases (RD) result in a wide variety of clinical presentations, and this creates a significant diagnostic challenge for health care professionals. We hypothesized that there exist a set of consistent and shared phenomena among all individuals affected by (different) RD during the time before diagnosis is established. OBJECTIVE: We aimed to identify commonalities between different RD and developed a machine learning diagnostic support tool for RD. METHODS: 20 interviews with affected individuals with different RD, focusing on the time period before their diagnosis, were performed and qualitatively analyzed. Out of these pre-diagnostic experiences, we distilled key phenomena and created a questionnaire which was then distributed among individuals with the established diagnosis of i.) RD, ii.) other common non-rare diseases (NRO) iii.) common chronic diseases (CD), iv.), or psychosomatic/somatoform disorders (PSY). Finally, four combined single machine learning methods and a fusion algorithm were used to distinguish the different answer patterns of the questionnaires. RESULTS: The questionnaire contained 53 questions. A total sum of 1763 questionnaires (758 RD, 149 CD, 48 PSY, 200 NRO, 34 healthy individuals and 574 not evaluable questionnaires) were collected. Based on 3 independent data sets the 10-fold stratified cross-validation method for the answer-pattern recognition resulted in sensitivity values of 88.9% to detect the answer pattern of a RD, 86.6% for NRO, 87.7% for CD and 84.2% for PSY. CONCLUSION: Despite the great diversity in presentation and pathogenesis of each RD, patients with RD share surprisingly similar pre-diagnosis experiences. Our questionnaire and data-mining based approach successfully detected unique patterns in groups of individuals affected by a broad range of different rare diseases. Therefore, these results indicate distinct patterns that may be used for diagnostic support in RD.
    • Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes

      Hain, Torsten; Ghai, Rohit; Billion, André; Kuenne, Carsten T; Steinweg, Christiane; Izar, Benjamin; Mohamed, Walid; Mraheil, Mobarak A; Domann, Eugen; Schaffrath, Silke; et al. (2012-04-24)
      Abstract Background Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans. Results The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model. Conclusion Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages.
    • Crystal structure of bacterial cytotoxic necrotizing factor CNFy reveals molecular building blocks for intoxication.

      Chaoprasid, Paweena; Lukat, Peer; Mühlen, Sabrina; Heidler, Thomas; Gazdag, Emerich-Mihai; Dong, Shuangshuang; Bi, Wenjie; Rüter, Christian; Kirchenwitz, Marco; Steffen, Anika; et al. (Springer, 2021-01-07)
      Cytotoxic necrotizing factors (CNFs) are bacterial single-chain exotoxins that modulate cytokinetic/oncogenic and inflammatory processes through activation of host cell Rho GTPases. To achieve this, they are secreted, bind surface receptors to induce endocytosis and translocate a catalytic unit into the cytosol to intoxicate host cells. A three-dimensional structure that provides insight into the underlying mechanisms is still lacking. Here, we determined the crystal structure of full-length Yersinia pseudotuberculosis CNFY . CNFY consists of five domains (D1-D5), and by integrating structural and functional data, we demonstrate that D1-3 act as export and translocation module for the catalytic unit (D4-5) and for a fused β-lactamase reporter protein. We further found that D4, which possesses structural similarity to ADP-ribosyl transferases, but had no equivalent catalytic activity, changed its position to interact extensively with D5 in the crystal structure of the free D4-5 fragment. This liberates D5 from a semi-blocked conformation in full-length CNFY , leading to higher deamidation activity. Finally, we identify CNF translocation modules in several uncharacterized fusion proteins, which suggests their usability as a broad-specificity protein delivery tool.
    • Crystal structure of NirF: insights into its role in heme d biosynthesis.

      Klünemann, Thomas; NIMTZ, MANFRED; Jänsch, Lothar; Layer, Gunhild; Blankenfeldt, Wulf; HZI, Helmholtz Zentrum für Infektionsforschung, GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (Wiley Online Open, 2020-04-07)
      Certain facultative anaerobes such as the opportunistic human pathogen Pseudomonas aeruginosa can respire on nitrate, a process generally known as denitrification. This enables denitrifying bacteria to survive in anoxic environments and contributes, for example, to the formation of biofilm, hence increasing difficulties in eradicating P. aeruginosa infections. A central step in denitrification is the reduction of nitrite to nitric oxide by nitrite reductase NirS, an enzyme that requires the unique cofactor heme d1 . While heme d1 biosynthesis is mostly understood, the role of the essential periplasmatic protein NirF in this pathway remains unclear. Here, we have determined crystal structures of NirF and its complex with dihydroheme d1 , the last intermediate of heme d1 biosynthesis. We found that NirF forms a bottom-to-bottom β-propeller homodimer and confirmed this by multi-angle light and small-angle X-ray scattering. The N termini are adjacent to each other and project away from the core structure, which hints at simultaneous membrane anchoring via both N termini. Further, the complex with dihydroheme d1 allowed us to probe the importance of specific residues in the vicinity of the ligand binding site, revealing residues not required for binding or stability of NirF but essential for denitrification in experiments with complemented mutants of a ΔnirF strain of P. aeruginosa. Together, these data suggest that NirF possesses a yet unknown enzymatic activity and is not simply a binding protein of heme d1 derivatives. DATABASE: Structural data are available in PDB database under the accession numbers 6TV2 and 6TV9.
    • Data Analysis Strategies for Microbiome Studies in Human Populations-a Systematic Review of Current Practice.

      Kleine Bardenhorst, Sven; Berger, Tom; Klawonn, Frank; Vital, Marius; Karch, André; Rübsamen, Nicole; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (ASM, 2021-02-23)
      Reproducibility is a major issue in microbiome studies, which is partly caused by missing consensus about data analysis strategies. The complex nature of microbiome data, which are high-dimensional, zero-inflated, and compositional, makes them challenging to analyze, as they often violate assumptions of classic statistical methods. With advances in human microbiome research, research questions and study designs increase in complexity so that more sophisticated data analysis concepts are applied. To improve current practice of the analysis of microbiome studies, it is important to understand what kind of research questions are asked and which tools are used to answer these questions. We conducted a systematic literature review considering all publications focusing on the analysis of human microbiome data from June 2018 to June 2019. Of 1,444 studies screened, 419 fulfilled the inclusion criteria. Information about research questions, study designs, and analysis strategies were extracted. The results confirmed the expected shift to more advanced research questions, as one-third of the studies analyzed clustered data. Although heterogeneity in the methods used was found at any stage of the analysis process, it was largest for differential abundance testing. Especially if the underlying data structure was clustered, we identified a lack of use of methods that appropriately addressed the underlying data structure while taking into account additional dependencies in the data. Our results confirm considerable heterogeneity in analysis strategies among microbiome studies; increasingly complex research questions require better guidance for analysis strategies.IMPORTANCE The human microbiome has emerged as an important factor in the development of health and disease. Growing interest in this topic has led to an increasing number of studies investigating the human microbiome using high-throughput sequencing methods. However, the development of suitable analytical methods for analyzing microbiome data has not kept pace with the rapid progression in the field. It is crucial to understand current practice to identify the scope for development. Our results highlight the need for an extensive evaluation of the strengths and shortcomings of existing methods in order to guide the choice of proper analysis strategies. We have identified where new methods could be designed to address more advanced research questions while taking into account the complex structure of the data.
    • Degradable magnesium implant-associated infections by bacterial biofilms induce robust localized and systemic inflammatory reactions in a mouse model.

      Rahim, Muhammad Imran; Babbar, Anshu; Lienenklaus, Stefan; Pils, Marina; Rohde, M; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017-06-01)
      Biomaterial-associated Pseudomonas aeruginosa biofilm infections constitute cascade of host immune reactions ultimately leading towards implant failure. Due to lack of relevant in vivo biofilm models, majority of the studies report host immune responses against free living or planktonic bacteria while bacteria in clinical situations live more frequently as biofilm communities than as single cells. Present study investigated host immune responses against biomaterial-associated P. aeruginosa biofilms in a clinically relevant mouse model. Previously, we reported metallic magnesium, a prospective biodegradable implant, to be permissive for bacterial biofilms in vivo even though it exhibits antibacterial properties in vitro. Therefore, magnesium was employed as biomaterial to investigate in vivo biofilm formation and associated host immune responses by using two P. aeruginosa strains and two mouse strains. P. aeruginosa formed biofilms on subcutaneously implanted magnesium discs. Non-invasive in vivo imaging indicated transient inflammatory responses at control sites whereas robust prolonged interferon-β (IFN-β) expression was observed from biofilms in a transgenic animal reporter. Further, immunohistology and electron microscopic results showed that bacterial biofilms were located in two dimensions immediately on the implant surface and at a short distance in the adjacent tissue. These biofilms were surrounded by inflammatory cells (mainly polymorphonuclear cells) as compared to controls. Interestingly, even though the number of live bacteria in various organs remained below detectable levels, splenomegaly indicated systemic inflammatory processes. Overall, these findings confirmed the resistance of biofilm infections in vivo to potentially antibacterial properties of magnesium degradation products. In vivo imaging and histology indicated the induction of both, local and systemic host inflammatory responses against P. aeruginosa biofilms. Even though the innate host immune defenses could not eliminate the local infection for up to two weeks, there was no apparent systemic bacteremia and all animals investigated survived the infection.
    • Der zlog-Wert als Basis für die Standardisierung von Laborwerten

      Hoffmann, Georg; Klawonn, Frank; Lichtinghagen, Ralf; Orth, Matthias; Helmholtz-Zentrum für Infektionsforshung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017-01-01)
      Zusammenfassung Hintergrund Im Zuge des deutschen E-Health-Gesetzes von 2016 wurde die DGKL aufgefordert, Vorschläge für die standardisierte Speicherung und Übermittlung von Labordaten zu erarbeiten. Wir schlagen dafür die in der Statistik weit verbreitete z-Transformation vor. Methoden Man erhält mit diesem Verfahren einen Relativwert, der angibt, um wie viele Standardabweichungen ein Messwert vom Mittelwert des Referenzkollektivs abweicht. Anhand realer Daten belegen wir die Annahme, dass die Werte gesunder Referenzpersonen durch logarithmische Transformation einer Normalverteilung angenähert werden können. Ergebnisse Kennt man somit die Unter- und Obergrenze UG und OG des Referenzintervalls, so kann man jedes Laborergebnis mit folgender Gleichung transformieren: Der zlog-Wert ist leicht interpretierbar: Sein Referenzintervall liegt methodenunabhängig stets zwischen –1,96 und +1,96; stark erniedrigte oder erhöhte Laborergebnisse führen zu zlog-Werten um –5 bzw. +5. Für eine intuitive Befunddarstellung kann man zlog-Werte auch in eine kontinuierliche Farbskala, z. B. von Blau über Weiß bis Orange umrechnen. Mithilfe der Umkehrfunktion lässt sich aus dem zlog-Wert auch das theoretische Resultat einer Messmethode mit einem anderen Referenzintervall berechnen: Schlussfolgerung Unser Standardisierungsvorschlag ist ein leicht realisierbarer und effektiver Beitrag zur Verbesserung der Datenqualität und Patientensicherheit im Rahmen des E-Health-Gesetzes. Es wird gefordert, dass alle Labore künftig zusätzlich zum Originalwert den zlog-Wert zur Verfügung stellen und dass in die Protokolle für die elektronische Labordatenübertragung (HL7, LDT) ein eigenes Feld für diesen zusätzlichen Wert eingefügt wird.
    • Design and characterization of dietary assessment in the German National Cohort.

      Knüppel, Sven; Clemens, Matthias; Conrad, Johanna; Gastell, Sylvia; Michels, Karin B; Leitzmann, Michael; Krist, Lilian; Pischon, Tobias; Krause, Gerard; Ahrens, Wolfgang; et al. (Springer Nature, 2019-01-15)
      BACKGROUND/OBJECTIVES: The aim of the study was to describe a novel dietary assessment strategy based on two instruments complemented by information from an external population applied to estimate usual food intake in the large-scale multicenter German National Cohort (GNC). As proof of concept, we applied the assessment strategy to data from a pretest study (2012-2013) to assess the feasibility of the novel assessment strategy. SUBJECTS/METHODS: First, the consumption probability for each individual was modeled using three 24 h food lists (24h-FLs) and frequencies from one food frequency questionnaire (FFQ). Second, daily consumed food amounts were estimated from the representative German National Nutrition Survey II (NVS II) taking the characteristics of the participants into account. Usual food intake was estimated using the product of consumption probability and amounts. RESULTS: We estimated usual intake of 41 food groups in 318 men and 377 women. The participation proportion was 100, 84.4, and 68.5% for the first, second, and third 24h-FL, respectively. We observed no associations between the probability of participating and lifestyle factors. The estimated distributions of usual food intakes were plausible and total energy was estimated to be 2707 kcal/day for men and 2103 kcal/day for women. The estimated consumption frequencies did not differ substantially between men and women with only few exceptions. The differences in energy intake between men and women were mostly due to differences in estimated daily amounts. CONCLUSIONS: The combination of repeated 24h-FLs, a FFQ, and consumption-day amounts from a reference population represents a user-friendly dietary assessment approach having generated plausible, but not yet validated, food intake values in the pretest study
    • Development of a data generator for multivariate numerical data with arbitrary correlations and distributions

      Vahldiek, Kai; Zhou, Libing; Zhu, Wenfeng; Klawonn, Frank; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (IOS Press, 2021-01-01)
      Artificial or simulated data are particularly relevant in tests and benchmarks for machine learning methods, in teaching for exercises and for setting up analysis workflows. They are relevant when real data may not be used for reasons of data protection, or when special distributions or effects should be present in the data to test certain machine learning methods. In this paper a generator for multivariate numerical data with arbitrary marginal distributions and – as far as possible – arbitrary correlations is presented. The data generator is implemented in the open source statistics software R. It can also be used for categorical variables, if data are generated separately for the corresponding characteristics of a categorical variable. Additionally, outliers can be integrated. The use of the data generator is demonstrated with a concrete example.
    • Development of a Social Network for People Without a Diagnosis (RarePairs): Evaluation Study.

      Kühnle, Lara; Mücke, Urs; Lechner, Werner M; Klawonn, Frank; Grigull, Lorenz; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (JMIR publications, 2020-09-29)
      Background: Diagnostic delay in rare disease (RD) is common, occasionally lasting up to more than 20 years. In attempting to reduce it, diagnostic support tools have been studied extensively. However, social platforms have not yet been used for systematic diagnostic support. This paper illustrates the development and prototypic application of a social network using scientifically developed questions to match individuals without a diagnosis. Objective: The study aimed to outline, create, and evaluate a prototype tool (a social network platform named RarePairs), helping patients with undiagnosed RDs to find individuals with similar symptoms. The prototype includes a matching algorithm, bringing together individuals with similar disease burden in the lead-up to diagnosis. Methods: We divided our project into 4 phases. In phase 1, we used known data and findings in the literature to understand and specify the context of use. In phase 2, we specified the user requirements. In phase 3, we designed a prototype based on the results of phases 1 and 2, as well as incorporating a state-of-the-art questionnaire with 53 items for recognizing an RD. Lastly, we evaluated this prototype with a data set of 973 questionnaires from individuals suffering from different RDs using 24 distance calculating methods. Results: Based on a step-by-step construction process, the digital patient platform prototype, RarePairs, was developed. In order to match individuals with similar experiences, it uses answer patterns generated by a specifically designed questionnaire (Q53). A total of 973 questionnaires answered by patients with RDs were used to construct and test an artificial intelligence (AI) algorithm like the k-nearest neighbor search. With this, we found matches for every single one of the 973 records. The cross-validation of those matches showed that the algorithm outperforms random matching significantly. Statistically, for every data set the algorithm found at least one other record (match) with the same diagnosis. Conclusions: Diagnostic delay is torturous for patients without a diagnosis. Shortening the delay is important for both doctors and patients. Diagnostic support using AI can be promoted differently. The prototype of the social media platform RarePairs might be a low-threshold patient platform, and proved suitable to match and connect different individuals with comparable symptoms. This exchange promoted through RarePairs might be used to speed up the diagnostic process. Further studies include its evaluation in a prospective setting and implementation of RarePairs as a mobile phone app.
    • Diacylglycerol Kinase from Suspension Cultured Plant Cells 1

      Wissing, Josef B.; Wagner, Karl G. (1992-03)
    • Diacylglycerol Kinase from Suspension Cultured Plant Cells 1

      Wissing, Josef; Heim, Sabina; Wagner, Karl G. (1989-08)